Section 2 - Primary Structure

To best appreciate the contents of this chapter you need to INTERACTIVELY EXAMINE a number of amino acid structures. If you haven't done so already, we STRONGLY URGE you to install the FREE molecular viewer software, RasMol and configure it to be automatically invoked by chemical/MIME. See our Technology Page to find out how.

Proteins consist of one or more polypeptide chains, each of which is a linear polymer of amino acid residues. Twenty types of amino acid occur naturally in proteins. A polypeptide can be defined simply by its sequence of amino acids. This sequence is referred to as the primary structure. The primary structure of a protein contains all the necessary information required for the manifestation of higher, three-dimensional levels of structure.

The Amino Acids

Single and 3-Letter Codes for Amino Acids - Learn Them!
Diagrams of the 20 Amino Acids have been provided by PPS student Jens Loesel (Thymine Group).

The following three tutorials on the amino acids include interactive molecules, which you can view with RasMol.

A Tutorial on the Amino Acids, by Sami Raza
Properties of the Amino Acids, by Jon Cooper
Tutorial on the Amino Acids, by PPS Consultant Alan Ward, Newcastle University Department of Microbiology. This material also includes an interactive Kinemage.

The following resource contains interactive molecules for use with the Alchemy mol format.

The Amino Acids, at the Free University of Berlin, by Vera Heinau and Burkhard Kirste

Summary of Amino Acid Properties

The different roles amino acids play within proteins
Here is a useful directory of amino acid properties (and a text version) by Ronald C. Beavis and David Fenyo, Skirball Institute Protein Chemistry Laboratory
Chirality of Aminoacids - the chemist's view by Luis P. Candeias of the Adenine Group

Implications of Primary Structure

Molecular Viewers

Rasmol

If you do not have yet have Rasmol, refer to the information under the Technology Index, which includes links telling you how to (1) get and install Rasmol and (2) configure your WWW browser so that it automatically invokes Rasmol when you click on an appropriate link (i.e. the URL of a pdb-format molecular structure file). Then return to the material above.

Kinemage

If you have Mage installed and your browser configured, then the Kinemages for Chapter 1 of Branden and Tooze will be of interest. This page indexing the B&T kinemages has been set up by Gail Schuman of Brookhaven Structural Biology. Again, refer to the help in the PPS Technology Index if necessary.